Confocal microscopy involves scanning tissue to produce microscopic sectional images of surface or subsurface tissue. Such microscopic imaged sections may be made in-vivo and can image tissue at cellular resolutions. Examples of confocal scanning microscopes are found in U.S. Pat. Nos. 5,788,639 and 5,880,880, and in articles by Milind Rajadhyaksha et al., “In vivo Confocal Scanning Laser Microscopy of Human Skin: Melanin provides strong contrast,” The Journal of Investigative Dermatology, Volume 104, No. 6, June 1995, pages 1-7, and by Milind Rajadhyaksha et al., “Confocal laser microscope images tissue in vivo,” Laser Focus World, February 1997, pages 119-127. These systems have confocal optics which direct light to the patient's tissue and image tissue sections from the returned reflected light. These confocal systems, although useful for microscopic examination of a tissue lesion or other abnormal tissue, have no capability for identifying locations on the surface of the tissue where the imaged lesion is within the tissue. Without such identification, the physician does not know after imaging the particular locations in the imaged tissue to carry out treatment of the lesion viewed in the images. Such treatment may include excising the tissue from the patient, radiation therapy, or ablation. Since treatment can harm healthy tissue which may lie near a lesion, precise location of the lesion is of importance. Also, without the capability to identify on the tissue surface the locations of an imaged lesion, it may be difficult for a physician to locate the lesion in future examinations for observing possible changes in the condition of the tissue when treatment of the lesion is deferred or is non-invasive.